Beyond Edman Degradation: Algorithmic De novo Protein Sequencing of Monoclonal Antibodies
University of California, San Diego –
The characterization and engineering of monoclonal antibodies is usually preceded by time-consuming Edman/cDNA sequencing steps for determination of the heavy and light chain sequences – a low-throughput pipeline that does not address post-translational modifications. In a departure from these platforms, we have developed the Comparative Shotgun Protein Sequencing (CSPS) suite of algorithms – a mass spectrometry based protein sequencing approach resulting in over 95% sequence coverage and automatic discovery of unexpected post-translational modifications. In contrast with the current multiple-week duration of typical sequencing projects, CSPS delivers additional functionality while reducing the time required to sequence an antibody to under 72 hours, a dramatic reduction as compared to the average 2-4 months for classical Edman sequencing of an entire antibody. While we demonstrate CSPS on monoclonal antibodies, the underlying techniques are not antibody-specific and the results indicate that CSPS has the potential to be a disruptive technology for all protein sequencing applications.
Date: 2009-Apr-07 Time: 14:00:00 Room: 336
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.